MINO)PROPYLAMINE]-3,4,9,10-PERYLENETETRACARBOXYLIC DIIMIDE, A DICATIONIC PERYLENE DYE FOR RAPID PRECIPITATION AND QUANTITATION OF TRACE AMOUNTS OF DNA

A novel dicationic dye with a polycyclic aromatic perylene core and fl exible cationic side chains-N, mino)propylamine]-3,4,9,10-perylenetetr acarboxylic diimide-termed ''DAPER,'' was synthesized and characterize d. The dye appears to exist in a highly stacked form in aqueous soluti on. DAPER precipitates extremely low concentrations of DNA very rapidl y, efficiently, and with a stoichiometry of one tightly bound dye per DNA base pair, corresponding to a neutral complex. Precipitation may o ccur due to side-by-side association between the polyanionic DNA helix and polycationic dye stacks. DNA precipitation by DAPER is less sensi tive to DNA concentration and length, and prevailing salt concentratio ns, than precipitation with ethanol or propanol. DAPER can be quantita tively extracted from DNA into a standard phenol:chloroform mixture un der slightly alkaline conditions. The recovered DNA is suitable for tr eatment with enzymes typically used in DNA sequencing procedures. The amount of DNA precipitated is accurately determined by visible absorpt ion or fluorescence spectroscopic analyses of the phenol:chloroform ex tracts, Several samples of DNA can be precipitated, recovered, and qua ntitated in about 1 h using standard microscale procedures and equipme nt. The unique qualities of DAPER provide the basis for a very sensiti ve, rapid, and versatile method for simultaneous precipitation and qua ntitation of microgram and submicrogram amounts of DNA. (C) 1996 Acade mic Press, Inc.